Explorer.exe not loading in startup

I have seen this twice in the last week. After a Malwarebyte scan (one was in safe mode and the other normal mode) on a system with misc Trojan's including Vundo and where MalwareByte requested a reboot to contine and remove the infected files and where I did not reboot as I ran Combofix after MalwareByte the systems booted up to a blank desktop. No taskbar, icons etc. If I ran Task Manager (Ctrl/Alt/Del) I could manually start Explorer and teh system worked fine until another reboot. After hours researching the problem I gave up. Any Ideas? Could this be because I did not reboot when asked to by MalwareByte and or possible ComboFix stopping certain unrecognised services that Malwarebyte runs on reboot?